Hi Darshan
no, resection is probably trouble depending on how big it is.
The talairach_afd is the automated failure detection. I can see why it
would give a warning for the resected dataset, but Vincent: you should
visually inspect your registration. It's not usually wrong when it warns,
and f
Sorry, but no.
On Wed, 2012-02-15 at 13:50 -1000, Jeff Sadino wrote:
> Hello,
>
>
> I have 200 subjects and I am analyzing their cortex in qdec. I have
> several subjects that have poor cortical surfaces on a local basis.
> Is there a way for exclude just one area for just one subject during
I am having the same error with one of my datasets . This subject has a good
part of the brain resected . Does Freesurfer
have problems dealing with partially resected brain datasets?
- Original Message -
I am having trouble with 2 scans that exit with errors. Both have the same
error:
Hi Jie
have you tried visualizing them in freeview or tkmedit? The .img/hdr files
won't have enough information to specify direction cosines without an
associated .mat file. Does that exist? Does BrainSuite know how to read it?
Bruce
On Wed, 15 Feb 2012, Jie Shi wrote:
> Hi, experts. I have
Hi, experts. I have recently used mri_convert to convert some dicom files
into both .nii and .img. But when observing in BrainSuite, I found the
image orientation of the .nii and .img was not consistent. Any idea about
the problem and how to make them same? Thanks a lot.
Jie
__
what viewer did you use to decide that they weren't consistent?
On Wed, 15
Feb 2012, Jie Shi wrote:
> Hi, experts. I have recently used mri_convert to convert some dicom files
> into both .nii and .img. But when observing, I found the image orientation
> of the .nii and .img was not consistent. A
Hi, experts. I have recently used mri_convert to convert some dicom files
into both .nii and .img. But when observing, I found the image orientation
of the .nii and .img was not consistent. Any idea about the problem and how
to make them same? Thanks a lot.
Jie
Hello,
I have 200 subjects and I am analyzing their cortex in qdec. I have
several subjects that have poor cortical surfaces on a local basis. Is
there a way for exclude just one area for just one subject during qdec
analysis? For example, on some images, the patient nose is in their
occipital
I am having trouble with 2 scans that exit with errors. Both have the same
error:
talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED***
This is actually preceded by a message stating that talairach.xfm already
exists and will not be copied. If I use the --clean-tal option
Weird. Glad it got fixed, let us know if you have any more trouble.
On Wed, 15 Feb 2012, Chris Watson wrote:
> Actually, it now works when I re-source my .bash_profile and .bashrc files.
> Not sure why that would be.
> Chris
>
> Chris Watson wrote:
>> Yes, the same error.
>> Chris
>>
>> Anas
Actually, it now works when I re-source my .bash_profile and .bashrc
files. Not sure why that would be.
Chris
Chris Watson wrote:
> Yes, the same error.
> Chris
>
> Anastasia Yendiki wrote:
>
>> When you run that bet command line outside of trac-all, does it give
>> you the same error?
>>
>>
Yes, the same error.
Chris
Anastasia Yendiki wrote:
>
> When you run that bet command line outside of trac-all, does it give
> you the same error?
>
> On Wed, 15 Feb 2012, Chris Watson wrote:
>
>> Here's output from mri_info:
>> [freesurfer@occipital dmri]$ mri_info lowb.nii.gz
>> Volume informat
When you run that bet command line outside of trac-all, does it give you
the same error?
On Wed, 15 Feb 2012, Chris Watson wrote:
> Here's output from mri_info:
> [freesurfer@occipital dmri]$ mri_info lowb.nii.gz
> Volume information for lowb.nii.gz
> type: nii
> dimensions: 96 x 96
Here's output from mri_info:
[freesurfer@occipital dmri]$ mri_info lowb.nii.gz
Volume information for lowb.nii.gz
type: nii
dimensions: 96 x 96 x 56
voxel sizes: 2.5000, 2.5000, 2.5000
type: FLOAT (3)
fov: 240.000
dof: 0
xstart: -120.0, xend:
Hey Chris - That is strange. The FSLOUTPUTTYPE would've been my first
guess, too. Does this lowb.nii.gz actually exist? Anything looks strange
when you run mri_info/freeview/fslview on it?
a.y
On Wed, 15 Feb 2012, Chris Watson wrote:
> Hello, in running trac-all -prep, I get an error saying t
Hello, in running trac-all -prep, I get an error saying that it can't
open "lowb.nii.gz.hdr":
fslroi
/raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/dwi.nii.gz
/raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz
0 1
fslmaths
/raid2/fmri8/fontan/volu
I have a question about the retinotopy analysis in freesurfer 5. I was
following these instructions :
http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis
with some minor edits because we don't have eccen data. And now I'm
ready
to view the data, but I'm confused by what I
It looks like you want (PF+PM)-(CF+CM) which would correspond to [0 0 0
0 1 1 -1 -1]/2. This just averages the slopes for F&M in each group,
then takes the difference between the average slopes.
doug
Katherine Reiter wrote:
> Hey freesurfers,
>
> I'm interested in running an interaction between
When I look at them with the more command on a linux machine, I see 2
lines in bval and 6 lines in bvec. Most likely this is a problem with the
text files being created with a windows program like excel and not having
unix-compatible end-of-line characters. It's been discussed a few times in
t
Hey freesurfers,
I'm interested in running an interaction between a continuous and
categorical variable, covarying for another categorical variable. I
understand that this analysis is not possible through the QDEC GUI so I am
working through the command line group analysis and setting up the contr
Hello,
I have run the following successfully, but when I have moved on to other
brains I get:
mri_label2vol --seg chuman_1.mgz --temp orig.mgz --regheader >
chuman_1.mgz --o chuman_1.conf.mgz
MRIalloc: could not allocate 975187978 frame
Cannot allocate memory
I am running a Mac Pro with 8GB R
Oh, sorry, I misread your email. I thought you had said you did positive
and now wanted to do negative. I don't think there is a way to easily go
from abs to pos or neg, you'll have to re-run.
doug
Govindarajan, Koushik Athreya wrote:
> Ok. But when I view them using tksurfer, absolute contrast
Ok. But when I view them using tksurfer, absolute contrast gives me both
positive and negative contrast clusters. Even if I copy the csd files and
change the header information, could I view just positive or negative
significant clusters on tksurfer?
Many Thanks for your help
Regards
Koushik
_
In principal, it should be the same correction as for the positive as
the simulation should be symmetrical across sign. But
mechanically/programatically, I don't have an easy way to do it. You can
copy the csd files to a new name and change the sign listed in the header.
doug
Govindarajan, Kous
Many Thanks for that Doug. It worked great. I do have another question for you
about monte carlo simulation. Say I run a simulation with an absolute contrast
initially. After the analysis is done, if I need results for a negative
contrast, is there a way to do that after the simulation or does i
Dear all,
I completed my DTI group analysis at subcortical level on the CVS space and
found clusters that survived by multiple comparisons. The results shows that FA
is decreasing in patients vs. controls.
I used then the same subject to do a structural group analysis to compare the
cortical
Try running it with --no-aseg.
doug
Adam David Felton wrote:
> Hello,
>
> I have run into an error while trying to make an average subject using
> 200 scans.
>
> When I ran this command I got an error:
> *make_average_subject --xform talairach.xfm --out 200avgsub --subjects*
>
> The error:
>
>
Hi Koushik, download this file and copy it into the mri/transforms directory
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/talairach.xfm
Then rerun mri_glmfit-sim with the --no-sim option so that it picks up
where it left off. You will need to give the "csdbase" which you passed
i
Hi Minjie,
The pathstats.byvoxel.txt gives the statistics of the higest probability
streamline of the posterior distribution of the tract and the
pathstats.overall.txt gives you average diffusion values for the whole
tract.
Please refer to the following:
http://surfer.nmr.mgh.harvard.edu/fswiki/
Hello freesurfer group,
I'm having trouble in the fixing bad output from the talairach registration
step. When I click on the "Save Reg" button to save a transformation that I
make the console just hangs on this message "UnZeroing CRAS for fstal
output xfm".
Anyone have any ideia what the problem
Hello group,
I am running the multiple comparisons simulation after my mri_glmfit
finished. I see that it went through all the iterations and then quit with the
following error message it could not find the talairach.xfm file in my average
brain. I did not use the fsaverage and instead
Dear Doug,
Can I run the mri_volcluter without --reg ?
I am asking this because when I run:
mri_glmfit-sim \
--glmdir GroupAnalysis_ADC.glmdir \
--grf 3 neg \
--cwpvalthresh .05 \
--overwrite
gives me the following error (I also attached the log file):
Also, does ne
Hi Doug,
By "more exactly location" I want to say that I would like to have the MNI
coordinates and also the annotation location or the nearst cortical label (for
example precentral or lateraloccipital, etc).
Also,after I ran the mri_segstatsI don't have the MNI coordinates.
Thanks for help
Sorry for bothering you again,
I have another error now: "Error: bvecs and bvals don't have the same
number of entries".
Visually my bval/bvec files seem ok to me. I can't find the problem.
I attach the files, could you please take a look on them?
Thank you very much,
Tanja.
On Tue, Feb 14, 2012
Hi EK
looks like an N3 problem. You might want to ask on the appropriate MNI
list.
cheers
Bruce
On Wed, 15 Feb 2012, EK Kim wrote:
Hello, Freesurfers,
I got an error message when I trying to use recon-all function in freesurfer
on the XUbuntu system installed on the VirtualBox on a Windows
it sounds like you ran out of memory. How much RAM do you have on your
machine?
On Tue, 14 Feb 2012, Adam David Felton wrote:
Hello,
I have run into an error while trying to make an average subject using 200
scans.
When I ran this command I got an error:
make_average_subject --xform talairac
Hello, Freesurfers,
I got an error message when I trying to use recon-all function in
freesurfer
on the Mandriva 2008 system installed on a Linux Dell precision T3500
Machine.
I was unable to find an answer in the mailing list.
my SUBJECTS_DIR is :
/neurospin/grip/protocols/MRI/childrenNS5_7y_Mon
Hi Joshua,
The "correct" way to obtain binarized maps would be to visit each
voxel in turn, compute the probability that it belongs to each of the
subfieds, and pick the subfield with the highest such probability.
Having said that, it should not be the case that there are two or more
subfields wi
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